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annotate README.rst @ 5:14561eb803a5 draft

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author peterjc
date Fri, 21 Oct 2016 10:55:40 -0400
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1 Galaxy Wrapper for GMAP
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2 =======================
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3
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4 This wrapper is copyright 2011, 2013 by Jim Johnson (Minnesota Supercomputing
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5 Institute, University of Minnesota).
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6 Revisions copyright 2016 by Peter Cock (The James Hutton Institute, UK).
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7
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8 This Galaxy wrapper is available from the Galaxy Tool Shed at:
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9
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10 toolshed.g2.bx.psu.edu/view/jjohnson/gmap
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11
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12 GMAP applications and citation info are available from:
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13 ttp://research-pub.gene.com/gmap/
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14
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15 Manual GMAP installation instructions are in the README file in the download,
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16 and online: http://research-pub.gene.com/gmap/src/README
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18
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19 History
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20 =======
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21
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22 ======= ======================================================================
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23 Version Changes
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24 ------- ----------------------------------------------------------------------
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25 v2.0.0 - Initial release, for GMAP version 2011-10-07 (by JJ, October 2011).
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26 v2.0.1 - Updated for GMAP version 2011-11-30 (by JJ, November 2011).
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27 v3.0.0 - Work in progress for GMAP version 2013-05-09 (by JJ, June 2013),
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28 never released to the main Galaxy Tool Shed.
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29 v3.0.1 - Various style updates (Peter Cock, October 2016).
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30 ======= ======================================================================
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31
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32
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33 Automated Installation
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34 ======================
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35
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36 This should be straightforward using the Galaxy Tool Shed, which should be
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37 able to automatically install GMAP as well.
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38
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39
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40
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41 Manual Installation
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42 ===================
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43
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44 GMAP and GSNAP use added datatypes:
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45
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46 - add datatype definition file: ``lib/galaxy/datatypes/gmap.py``
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47
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48 - add the following import line to: ``lib/galaxy/datatypes/registry.py``::
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49
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50 import gmap # added for gmap tools
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51
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52 - add to ``datatypes_conf.xml``::
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53
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54 <!-- Start GMAP Datatypes -->
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55 <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB" display_in_upload="False"/>
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56 <datatype extension="gmapsnpindex" type="galaxy.datatypes.gmap:GmapSnpIndex" display_in_upload="False"/>
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57 <datatype extension="iit" type="galaxy.datatypes.gmap:IntervalIndexTree" display_in_upload="True"/>
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58 <datatype extension="splicesites.iit" type="galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree" display_in_upload="True"/>
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59 <datatype extension="introns.iit" type="galaxy.datatypes.gmap:IntronsIntervalIndexTree" display_in_upload="True"/>
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60 <datatype extension="snps.iit" type="galaxy.datatypes.gmap:SNPsIntervalIndexTree" display_in_upload="True"/>
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61 <datatype extension="tally.iit" type="galaxy.datatypes.gmap:TallyIntervalIndexTree" display_in_upload="True"/>
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62 <datatype extension="gmap_annotation" type="galaxy.datatypes.gmap:IntervalAnnotation" display_in_upload="False"/>
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63 <datatype extension="gmap_splicesites" type="galaxy.datatypes.gmap:SpliceSiteAnnotation" display_in_upload="True"/>
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64 <datatype extension="gmap_introns" type="galaxy.datatypes.gmap:IntronAnnotation" display_in_upload="True"/>
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65 <datatype extension="gmap_snps" type="galaxy.datatypes.gmap:SNPAnnotation" display_in_upload="True"/>
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66 <datatype extension="gsnap_tally" type="galaxy.datatypes.gmap:TallyAnnotation" display_in_upload="True"/>
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67 <datatype extension="gsnap" type="galaxy.datatypes.gmap:GsnapResult" display_in_upload="True"/>
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68 <!-- End GMAP Datatypes -->
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69
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70 Tools:
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71
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72 - GMAP_Build - create a GmapDB set of index files for a reference sequence and optional set of annotations
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73 - GMAP - map sequences to a reference sequence GmapDB index
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74 - GSNAP - align sequences to a reference and detect splicing
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75
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76 Add to ``tool_conf.xml`` (probably in the "NGS: Mapping" section)::
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77
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78 <tool file="gmap/gmap.xml" />
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79 <tool file="gmap/gsnap.xml" />
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80 <tool file="gmap/gmap_build.xml" />
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81 <tool file="gmap/snpindex.xml" />
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82 <tool file="gmap/iit_store.xml" />
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83
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84 Admin built cached gmapdb indexes defined in ``tool-data/gmap_indices.loc``
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85
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86
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87 TODO
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88 ====
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89
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90 - Add classes to ``gmap.py``
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91
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92 - CmetIndex - an index created by cmetindex
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93 - AtoiIndex - an index created by atoiindex
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94
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95 - Add tally creation
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96
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97 - gsnap default output -> gsnap_tally -> iit_store
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98
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99 - Add goby support
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100
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101 - Should add separate tools and datatypes for goby
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102 - GSNAP goby output relies on goby input, might be better to have a separate gsnap tool for goby
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103
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104 - Possibly add Tools:
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105
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106 - get_genome - retrieves from a gmapdb
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107 - cmetindex - create methylcytosine index
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108 - atoiindex - create A-to-I RNA editing index